Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
25,372
datasets available to search
ShareScore release 0.7.1
Dataset results
25,372 results for “Transcriptomics”
Novel sex-specific genes and diverse interspecific expression in the antennal transcriptomes of ithomiine butterflies"
<p>The following repository contains both the genomic and functional annotations for 4 Ithomiini species. Data that was used in GBE paper "Novel sex-specific genes and diverse interspecific expression in the antennal transcriptomes of ithomiine butterflies".</p>
Experiment results of the article of "Enhancing spatial domain detection in spatial transcriptomics with EnSDD"
<p>The experiment results for the reproducibility of the article of "Enhancing spatial domain detection in spatial transcriptomics with EnSDD"</p>
Global Transcriptomic Analysis of Topical Sodium Alginate Protection Against Peptic Damage in An In Vitro Model of Treatment-Resistant Gastroesophageal Reflux Disease
<p>PA= pepsin + Acid; "Sham + PA" means "Pretreatment + Treatment"</p> <p><span>Breakthrough symptoms </span>are thought to occur in roughly half of <span>all </span>gastroesophageal reflux disease (GERD) patients despite maximal acid suppression (proton pump inhibitor, PPI) therapy. Topical alginates have recently been shown to enhance mucosal defense against acid-pepsin insult during GERD. We aimed to examine potential alginate protection of transcriptomic changes in a cell culture model of PPI recalcitrant GERD. Immortalized normal-derived human esophageal epithelial cells underwent pretreatment with commercial alginate-based anti-reflux medications (Gaviscon Advance or Gaviscon Double Action), a matched-viscosity placebo control, or pH 7.4 buffer (sham) alone for 1 minute, followed by exposure to pH 6.0+pepsin or buffer alone for 3 minutes. RNA sequencing was conducted, and Ingenuity Pathway Analysis was performed with a false discovery rate of ≤0.01, and absolute fold-change of ≥<span>1.3. Pepsin-acid exposure disrupted gene expressions associated with epithelial barrier function, chromatin structure</span>, carcinogenesis, and inflammation<span>. Alginate formulations demonstrated protection by mitigating these changes and promoting extracellular matrix repair, downregulating proto-oncogenes, and enhancing tumor suppressor expression. </span>These data suggest molecular mechanisms by which alginates provide topical protection against injury during weakly acidic reflux and support a potential role for alginates in prevention of GERD-related carcinogenesis.</p>
Phylum Cnidaria (Anthozoa: Hexacorallia) CANTATA Transcriptomes
<p>CANTATA is a Community bAsed Non-bilaTeriAn Transcriptome Archive aiming to provide an archive of non-bilaterian transcriptomic resources assembled and annotated in a standardized manner.</p><p> </p><p>In this repository, we provide the transcriptomes assemblies corresponding to the Phylum Cnidaria (Class Anthozoa, Subclass Hexacorallia).</p><p> </p><p>Currently, the following species are available:</p><ul><li><i>Acropora aculeus</i></li><li><i>Acropora cervicornis</i></li><li><i>Acropora digitifera</i></li><li><i>Acropora millepora</i></li><li><i>Acropora tenuis</i></li><li><i>Actinia tenebrosa</i></li><li><i>Agaricia lamarcki</i></li><li><i>Alveopora japonica</i></li><li><i>Anemonia sulcata</i></li><li><i>Anemonia viridis</i></li><li><i>Anthopleura dowii</i></li><li><i>Anthopleura elegantissima</i></li><li><i>Antipathes caribbeana</i></li><li><i>Aulactinia veratra</i></li><li><i>Calliactis polypus</i></li><li><i>Coelastrea aspera</i></li><li><i>Condylactis gigantea</i></li><li><i>Corynactis australis</i></li><li><i>Ctenactis echinata</i></li><li><i>Cyphastrea serailia</i></li><li><i>Dipsastraea rotumana</i></li><li><i>Edwardsiella carnea</i></li><li><i>Entacmaea quadricolor</i></li><li><i>Favites acuticollis</i></li><li><i>Fungia fungites</i></li><li><i>Galaxea astreata</i></li><li><i>Goniastrea retiformis</i></li><li><i>Goniopora columna</i></li><li><i>Heteractis crispa</i></li><li><i>Lobactis scutaria</i></li><li><i>Megalactis griffithsi</i></li><li><i>Montastraea cavernosa</i></li><li><i>Montipora aequituberculata</i></li><li><i>Montipora capitata</i></li><li><i>Montipora digitata</i></li><li><i>Nematostella vectensis</i></li><li><i>Palythoa caribaeorum</i></li><li><i>Palythoa variabilis</i></li><li><i>Plesiastrea versipora</i></li><li><i>Plumapathes pennacea</i></li><li><i>Pocillopora damicornis</i></li><li><i>Porites astreoides</i></li><li><i>Porites australiensis</i></li><li><i>Porites lobata</i></li><li><i>Porites lutea</i></li><li><i>Protopalythoa variabilis</i></li><li><i>Pseudodiploria strigosa</i></li><li><i>Rhodactis indosinensis</i></li><li><i>Seriatopora hystrix</i></li><li><i>Siderastrea siderea</i></li><li><i>Stichodactyla haddoni</i></li><li><i>Stichodactyla helianthus</i></li><li><i>Tubastraea coccinea</i></li></ul><p>The details about the read files used to assemble each transcriptome can be found at the CANTATA repository (https://gitlab.lrz.de/palmuc/cantata)</p>
The usage of transcriptomics datasets as sources of Real-World Data for clinical trialling -- Supplementary Data
Open the record for dataset details and reuse information.
Liver transcriptome analysis reveals PSC-attributed gene set associated with fibrosis progression
Open the record for dataset details and reuse information.
Ice recrystallization inhibitors enable efficient cryopreservation of induced pluripotent stem cells: A functional and transcriptomic analysis
<p><span>The successful use of human induced pluripotent stem cells (iPSCs) for research or clinical applications requires the development of robust, efficient, and reproducible cryopreservation protocols. After cryopreservation, the survival rate of iPSCs is suboptimal and cell line dependent. We assessed the use of ice recrystallization inhibitors (IRIs) for cryopreservation of human iPSCs<span>. A toxicity screening study was performed to assess specific small-molecule carbohydrate-based IRI and concentrations for further evaluation.</span> Then, a cryopreservation study compared the cryoprotective efficiency of 15 mM IRIs in 5 % or 10 % DMSO-containing solutions and with CryoStor® CS10. Three iPSC lines were cryopreserved as single-cell suspensions in the cryopreservation solutions and post-thaw characteristics, including pluripotency and differential gene expression, were assessed. </span><span>W</span><span>e demonstrate the fitness-for-purpose of 15 mM IRI in 5 % DMSO as an efficient cryoprotective solution for iPSCs in terms of post-thaw recovery, viability, pluripotency, and transcriptomic changes. Given that this dataset is the first report where mRNA sequencing has been used to identify expression changes resulting from iPSCs cryopreservation, it has the potential to be used for molecular mechanism analysis relating to cryopreservation. IRIs can reduce DMSO concentrations, thereby improving the utility, effectiveness, and efficiency of cryopreservation. </span></p>
Ulkenia visurgenis Lng2 transcriptomic analysis
<p><span>Programming codes, intermediates files, transcript annotation spreadsheets and the final version of the assembled transcriptome developed for a transcriptional anaylisis of the thraustochytrid <em>Ulkenia visurgensis</em> Lng2.</span></p>
Data from: Blood transcriptomes reveal novel parasitic zoonoses circulating in Madagascar's lemurs
Zoonotic diseases are a looming threat to global populations, and nearly 75% of emerging infectious diseases can spread among wildlife, domestic animals and humans. A 'One World, One Health' perspective offers us an ideal framework for understanding and potentially mitigating the spread of zoonoses, and the island of Madagascar serves as a natural laboratory for conducting these studies. Rapid habitat degradation and climate change on the island are contributing to more frequent contact among humans, livestock and wildlife, increasing the potential for pathogen spillover events. Given Madagascar's long geographical isolation, coupled with recent and repeated introduction of agricultural and invasive species, it is likely that a number of circulating pathogens remain uncharacterized in lemur populations. Thus, it is imperative that new approaches be implemented for de novo pathogen discovery. To this end, we used non-targeted deep sequencing of blood transcriptomes from two species of critically endangered wild lemurs (Indri indri and Propithecus diadema) to characterize blood-borne pathogens. Our results show several undescribed vector-borne parasites circulating within lemurs, some of which may cause disease in wildlife, livestock and humans. We anticipate that advanced methods for de novo identification of unknown pathogens will have broad utility for characterizing other complex disease transmission systems.
Data from: Combined transcriptome and metabolome analysis identifies defence responses in spider-mite infested pepper
<p>Plants regulate responses towards herbivory through fine-tuning of defence-related hormone production, expression of defence genes and production of secondary metabolites. Jasmonic acid (JA) plays a key role in plant-herbivorous arthropod interactions. To understand how pepper responds to herbivory, leaf transcriptomes and metabolomes of two genotypes different in their susceptibility to spider mites, were studied. Mites induced both JA and salicylic acid (SA) signalling. However, mite infestation and exogenous JA resulted in distinct transcriptome profiles. Compared with JA, mites induced less differentially expressed genes involved in metabolic processes (except for genes involved in the phenylpropanoid pathway) and lipid metabolic processes. Furthermore, pathogen-related defence responses including WRKY transcription factors, were stronger induced upon mite infestation, likely as result of induced SA signalling. Untargeted analysis of secondary metabolites confirmed that JA treatment induced larger changes in metabolism than spider-mite infestation, resulting in a higher terpenoid and flavonoid production. The more resistant genotype exhibited a larger increase in endogenous JA and volatile and non-volatile secondary metabolites upon infestation, which could explain its stronger defence. Reasoning that in JA-SA antagonizing crosstalk, SA-defences are prioritized over JA-defences, we hypothesize that lack of SA-mediated repression of JA-induced defences could result in gain-of-resistance towards spider mites in pepper.</p>
Data from: De novo assembly of a tadpole shrimp (Triops newberryi) transcriptome and preliminary differential gene expression analysis
Next-generation sequencing techniques, such as RNA sequencing, have provided a wealth of genomic information for nonmodel species. Transcriptomic information can be used to quantify the patterns of gene expression, which can identify how environmental differences invoke organismal stress responses and provide a gauge in predicting species adaptability. In our study, we used RNA sequencing to characterize the first transcriptome from a naupliar tadpole shrimp (Triops newberryi) to identify the genes expressed during the early life history stages and which could be important for future genomic studies. RNA was extracted from naupliar T. newberryi that were reared in a laboratory-controlled setting and in two different water types, a native and a non-native condition. A total of six replicates, three per condition, were sequenced with the Illumina Hi-Seq 2000 achieving 365 M 50-nt reads. High-quality reads were produced and de novo assembly was used to construct a T. newberryi transcriptome that was approximately 24.8 M base pairs. More than 10 000 peptides were predicted from the assembly, and genes were sorted into gene ontology categories. The use of different water conditions allowed for a preliminary differential gene expression analysis in order to compare the changes in gene expression between conditions. There were 299 differentially expressed genes between water conditions that might serve as a focal point for future genomic studies of Triops acclimation to different environments. The Triops transcriptome could serve as vital genomic information for additional studies on Branchiopod crustaceans.
Data from: Transcriptome characterization and screening of molecular markers in ecologically important Himalayan species (Rhododendron arboreum)
Rhododendron arboreum is an ecologically prominent species, which also lends commercial and medicinal benefits in the form of palatable juices and useful herbal drugs. Local abundance and survival of the species under a highly fluctuating climate make it an ideal model for genetic structure and functional analysis. However, a lack of genomic data has hampered additional research. In the present study, cDNA libraries from floral and foliar tissues of the species were sequenced to provide a foundation for understanding the functional aspects of the genome and to construct an enriched repository that will promote genomics studies in the genera. Illumina's platform facilitated the generation of ∼100 million high-quality paired-end reads. De novo assembly, clustering, and filtering out of shorter transcripts predicted 113 167 non-redundant transcripts with an average length of 1164.6 bases. Of these, 71 961 transcripts were categorized based on functional annotations in the Gene Ontology database, whereby 5710 were grouped into 141 pathways and 23 746 encoded for different transcription factors. Transcriptome screening further identified 35 419 microsatellite regions, of which, 43 polymorphic loci were characterized on 30 genotypes. Seven hundred and nineteen transcripts had 811 high-quality single-nucleotide polymorphic variants with a minimum coverage of 10, a total score of 20, and SNP% of 50.
Data from: De novo sequencing and assembly of Azadirachta indica fruit transcriptome
Azadirachta indica (neem) is a unique, versatile and important tree species. Many parts of the plant are traditionally used as pesticide, insecticide, fungicide and for other medicinal purposes. Azadirachta fruits and seeds, a good source of oil, are widely used for agriculturally important pest management. Neem oil and its derivatives also support multiple cottage industries in India. Past efforts have been mostly concentrated towards identifying, characterizing and synthesizing one of its principal components, i.e. azadirachtin from seed kernels. Despite diverse use of the neem plant, a modern drug-development programme which systematically exploits the therapeutic ability of Azadirachta fruits remains to be fully established. Next generation sequencing technology that helps decode genomes and transcriptomes has transformational impact on medicine, agriculture, bio-fuel and biodiversity studies. Here, we report sequencing, assembly and analysis of Azadirachta fruit transcriptome using next-generation sequencing technology. We believe that our study shall offer valuable insights towards realizing the larger vision of understanding the key medicinally active compounds and their pathways.
Data from: Diurnal and nocturnal transcriptomic variation in the Caribbean staghorn coral, Acropora cervicornis
Reef-building corals experience large diel shifts in their environment, both externally due to changes in light intensity, predator activity and prey availability, and internally as a result of diel fluctuations in photosynthesis by their endosymbiotic algae, Symbiodinium. Diel patterns of tentacle behaviour, skeletal growth and gene expression indicate reactions of the coral animal in response to light and through circadian regulation. Some corals, such as the Caribbean Acroporas, have strong within-colony division of labour, including specialized fast-growing apical polyps, accompanied by large gene expression differences. Here we use RNA-seq to evaluate how diel changes in gene expression vary within the branching Caribbean staghorn coral, Acropora cervicornis, between branch tips and branch bases. Multifactor generalized linear model analysis indicated that 6% (3005) of transcripts were differentially expressed between branch tips and bases, while 1% (441) of transcripts were differentially expressed between day and night. The gene expression patterns of 220 transcripts were affected by both time of day and location within the colony. In particular, photoreceptors, putative circadian genes, stress response genes and metabolic genes were differentially expressed between day and night, and some of these, including Amcry1, tef and hebp2, exhibited location-specific regulation within the coral colony as well. These findings indicate that the genetic response of the coral to day and night conditions varies within the colony. Both time of day and location within the colony are factors that should be considered in future coral gene expression experiments.
Data from: Transcriptomics of host-specific interactions in natural populations of the parasitic plant purple witchweed (Striga hermonthica)
Host-specific interactions can maintain genetic and phenotypic diversity in parasites that attack multiple host species. Host diversity, in turn, may promote parasite diversity by selection for genetic divergence or plastic responses to host type. The parasitic weed purple witchweed [Striga hermonthica (Delile) Benth.] causes devastating crop losses in sub-Saharan Africa and is capable of infesting a wide range of grass hosts. Despite some evidence for host adaptation and host-by-Striga genotype interactions, little is known about intraspecific Striga genomic diversity. Here we present a study of transcriptomic diversity in populations of S. hermonthica growing on different hosts (maize [Zea mays L.] vs. grain sorghum [Sorghum bicolor (L.) Moench]). We examined gene expression variation and differences in allelic frequency in expressed genes of aboveground tissues from populations in western Nigeria parasitizing each host. Despite low levels of host-based genome-wide differentiation, we identified a set of parasite transcripts specifically associated with each host. Parasite genes in several different functional categories implicated as important in host–parasite interactions differed in expression level and allele on different hosts, including genes involved in nutrient transport, defense and pathogenesis, and plant hormone response. Overall, we provide a set of candidate transcripts that demonstrate host-specific interactions in vegetative tissues of the emerged parasite S. hermonthica. Our study shows how signals of host-specific processes can be detected aboveground, expanding the focus of host–parasite interactions beyond the haustorial connection.
Data from: Preadult life history variation determines adult transcriptome expression
Preadult determinants of adult fitness and behavior have been documented in a variety of organisms with complex life cycles, but little is known about expression patterns of genes underlying these adult traits. We explored the effects of differences in egg to adult development time on adult transcriptome and cuticular hydrocarbon variation in order to understand the nature of the genetic correlation between preadult development time and premating isolation between populations of Drosophila mojavensis reared in different host cactus environments. Transcriptome variation was analyzed separately in flies reared on each host and revealed that hundreds of genes in adults were differentially expressed (FDR P < 0.05) due to development time differences. For flies reared on pitaya agria cactus, longer preadult development times caused increased expression of genes in adults enriched for ribosome production, protein metabolism, chromatin remodeling, and regulation of alternate splicing and transcription. Baja California flies reared on organ pipe cactus showed fewer differentially expressed genes in adults due to longer preadult development time, but these were enriched for ATP synthesis and the TCA cycle. Mainland flies reared on organ pipe cactus with shorter development times showed increased transcription of genes enriched for mitochondria and energy production, protein synthesis, and glucose metabolism: adults with longer development times had increased expression of genes enriched for adult life span, cuticle proteins and ion binding, although most differentially expressed genes were unannotated. Differences due to population, sex, mating status, and their interactions were also assessed. Adult cuticular hydrocarbon profiles also showed shifts due to egg to adult development time, and were influenced by population and mating status. These results help to explain why preadult life history variation determines subsequent expression of the adult transcriptome along with traits involved with reproductive isolation and revealed previously undocumented connections between genetic and environmental influences over the entire life cycle in this desert insect.
Data from: The developmental transcriptomes of two sea biscuit species with differing larval types
Background: Larval developmental patterns are extremely varied both between and within phyla, however the genetic mechanisms leading to this diversification are poorly understood. We assembled and compared the developmental transcriptomes for two sea biscuit species (Echinodermata: Echinoidea) with differing patterns of larval development, to provide a resource for investigating the evolution of alternate life cycles. One species (Clypeaster subdepressus) develops via an obligately feeding larva which metamorphoses 3-4 weeks after fertilization; the other (Clypeaster rosaceus) develops via a facultatively feeding larva that can develop through metamorphosis entirely based on egg provisioning in under one week. Results: Overall, the two transcriptomes are highly similar, containing largely orthologous contigs with similar functional annotation. However, we found distinct differences in gene expression patterns between larvae of the two species. Larvae from C. rosaceus, the facultative planktotroph, turned genes on at earlier stages and had less differentiation in gene expression between larval stages, whereas, C. subdepressus showed a higher degree of stage-specific gene expression. Conclusion: This study is the first genetic analysis of a species with facultatively feeding larvae. Our results are consistent with known developmental differences between the larval types and raise the question of whether earlier onset of developmental genes is a key step in the evolution of a reduced larval period. By publishing a transcriptome for this rare, intermediate, larval type, this study adds developmental breadth to the current genetic resources, which will provide a valuable tool for future research on echinoderm development as well as studies on the evolution of development in general.
Data from: Impacts of salt stress on locomotor and transcriptomic responses in the intertidal gastropod Batillaria attramentaria
Salinity is one of the most crucial environmental factors that structures biogeographic boundaries of aquatic organisms, affecting distribution, abundance, and behavior. However, the association between behavior and gene regulation underlying acclimation to changes in salinity remains poorly understood. In this study, we investigated the effects of salinity stress on behavior (movement distance) and patterns of gene expression (using RNA-seq) of the intertidal gastropod Batillaria attramentaria. We examined responses to short- (1 hour) and long-term (30 day) acclimation to a range of salinities (43, 33 (control), 23, 13, and 3 Practical Salinity Units (PSU)). We found that the intertidal B. attramentaria is able to tolerate a broad range of salinity from 13 to 43 PSU, but not the acute low salinity of 3 PSU. Behavioral experiments showed that salt stress significantly influenced snails' movement, with lower salinity resulting in shorter movement distance. Transcriptomic analyses revealed critical metabolic pathways and genes potentially involved in acclimation to salinity stress, including ionic and osmotic regulation, signal and hormonal transduction pathways, water exchange, cell protection, and gene regulation or epigenetic modification. In general, our study presents a robust, integrative laboratory-based approach to investigate the effects of salt stress on a non-model gastropod, which is facing detrimental consequences of environmental change. The current genetic results provide a wealth of reference data for further research on mechanisms of ionic and osmotic regulation and adaptive evolution of this coastal gastropod.
Data from: Blue mussel (Genus Mytilus) transcriptome response to simulated climate change in the Gulf of Maine
<p>The biogeochemistry of the Gulf of Maine is rapidly changing in response to a changing climate, including rising temperatures, acidification, and declining primary productivity. These impacts are projected to worsen over the next hundred years and will apply selective pressure on populations of marine calcifiers. This study investigates the transcriptome expression response to these changes in ecologically and economically important marine calcifiers, blue mussels. Wild mussels (<i>Mytilus edulis</i> and <i>M. trossulus</i>) were sampled from sites spanning the Gulf of Maine and exposed to two different biogeochemical water conditions: i. present-day conditions in the Gulf of Maine and ii. simulated future conditions that included elevated temperature, increased acidity, and decreased food supply. Patterns of gene expression were measured using RNA-seq from 24 mussel samples and contrasted between ambient and future conditions. The net calcification rate, a trait predicted to be under climate-induced stress, was measured for each individual over a 2-week exposure period and used as a covariate along with gene expression patterns. Generalized linear models, with and without the calcification rate, were used to identify differentially expressed transcripts between ambient and future conditions. The comparison revealed transcripts that likely comprise a core stress response characterized by the induction of molecular chaperones, genes involved in aerobic metabolism, and indicators of cellular stress. Furthermore, the model contrasts revealed transcripts that may be associated with individual variation in calcification rate and suggest possible biological processes that may have downstream effects on calcification phenotypes, such as zinc-ion binding and protein degradation. Overall, these findings contribute to the understanding of blue mussel adaptive responses to imminent climate change and suggest metabolic pathways are resilient in variable environments.</p>
Transcriptome dataset to: Chemical genetics in Silene latifolia elucidate regulatory pathways involved in gynoecium development
<p>This collection contains RNA-seq data obtained from young flower buds of <em>Silene latifolia </em>for each sample in the main manuscript in triplicate (male, female, two generations of hermaphrodites). The RNA was isolated from adult plants of U15 population and two subsequent generations, made by full-sib mating (U15=15 generations, U16=16 generations, U17=17 generations). The petals and sepals were removed before RNA-isolation. To avoid the bias made by sampling of old flower buds, only the first flowers were always sampled. The deposited RNA-seq data were not processed. </p>
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.